VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed May 30 2012 - 08:56:42 CDT

And a dumb but effective solution I've used before: move an atom in your system that is irrelevant to your analysis to the exact location, and then make the atom selection around this atom.

I guess I'll start using the decent math method suggested by Axel.
___________________________

Yi (Yves) Wang
Duke University

On 2012-5-30, at 上午3:00, <peter.schmidtke_at_fr.netgrs.com> <peter.schmidtke_at_fr.netgrs.com> wrote:

> Dear Axel and other respondents,
>
> Thanks a lot for your hint. Indeed the equation of the sphere is the most elegant solution for what I need.
>
> Cheers.
>
> Peter
>
> -----Message d'origine-----
> De : owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] De la part de Pawel Kedzierski
> Envoyé : jeudi 24 mai 2012 19:45
> À : vmd-l_at_ks.uiuc.edu
> Objet : Re: vmd-l: TR: VMD atomselect with cartesian reference
>
>
>
> W dniu 24.05.2012 16:13, Axel Kohlmeyer pisze:
>> On Thu, May 24, 2012 at 9:16 AM,<peter.schmidtke_at_fr.netgrs.com> wrote:
>>> Dear VMD users/developers,
>>>
>>>
>>>
>>> I’d like to create a selection of atoms that is within a given
>>> distance from a point in 3D cartesian space (not a molecular object, atom or whatsoever).
>>>
>>>
>>>
>>> How can this be achieved in VMD/tcl? I’ve been searching around for
>>> documentation but was fairly unsuccessful.
>>>
>>> Basically I’d like to do something like :
>>>
>>> atomselect top “protein within 20.0 of {-1 1 0}”
>>>
>>>
>>>
>>> Where {-1 1 0} is the cartesian coordinate from which I’d like to do
>>> the measure.
>> nope. you can't do this. "within X of Y" requires Y to be a selection
>> of atoms. please see the documentation. computer software is brutally
>> literal.
>> it doesn't know how to do "the reasonable thing(tm)".
>>
>> what you *can* do is math with the coordinates.
>> for example you can try this (untested):
>>
>> atomselect top "protein and ( ((x+1.0)*(x+1.0)+(y-1.0)*(y-1.0) + z*z)< 400.0)"
> Or:
> 1. Add to your system, for example to the PDB file, a residue X with single atom X positioned where you want it; 2. Of course you will want to omit this atom from display with 'not resname X' or 'not name X' in the selection; 3. Then you simply use selection 'within 20 of name X and not name X' or so; 4. And using the move command for selection, you can position your reference atom X wherever you want.
> HTH,
> Pawel
>
>>
>> cheers,
>> axel.
>>
>>>
>>>
>>> Thanks in advance for your help.
>>>
>>>
>>>
>>> Best regards.
>>>
>>>
>>>
>>> Peter Schmidtke
>>
>>
>